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- PDB-6ex5: Staphylococcus aureus triple mutant of superoxide dismutase SodM -

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Basic information

Entry
Database: PDB / ID: 6ex5
TitleStaphylococcus aureus triple mutant of superoxide dismutase SodM
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / superoxide dismutase / cambialistic / Staphylococcus aureus / metalloenzyme
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / metal ion binding / cytoplasm
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn/Fe] 2 / Superoxide dismutase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBarwinska-Sendra, A. / Basle, A. / Waldron, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
Wellcome Trust098375/Z/12/Z United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: An evolutionary path to altered cofactor specificity in a metalloenzyme
Authors: Barwinska-Sendra, A. / Garcia, Y.M. / Sendra, K. / Basle, A. / Mackenzie, E.S. / Tarrant, E. / Card, P. / Tabares, L.C. / Bicep, C. / Un, S. / Kehl-Fie, T.E. / Waldron, K.J.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8714
Polymers45,7612
Non-polymers1102
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-11 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.979, 58.206, 128.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase


Mass: 22880.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: sodA, sodM, BER48_000119, BN1321_40056, CEJ93_07215, ERS072738_00830, ERS072840_00559, ERS073583_02338, ERS074020_00889, HMPREF3211_00238
Production host: Escherichia coli (E. coli)
References: UniProt: W8UU58, UniProt: Q2G261*PLUS, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 100 mM K thiocyanate, 30% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→43.12 Å / Num. obs: 44670 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 9.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2415 / CC1/2: 0.882 / % possible all: 99.9

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Processing

Software
NameClassification
GDAdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCV

2rcv


Resolution: 1.75→43.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.519 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21559 2281 5.1 %RANDOM
Rwork0.18399 ---
obs0.18555 42320 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--1.81 Å2-0 Å2
3----2.03 Å2
Refinement stepCycle: 1 / Resolution: 1.75→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 2 323 3559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193351
X-RAY DIFFRACTIONr_bond_other_d0.0020.022931
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9224561
X-RAY DIFFRACTIONr_angle_other_deg0.96936842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71625.367177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63915550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.71158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6011.5921588
X-RAY DIFFRACTIONr_mcbond_other0.6011.5911587
X-RAY DIFFRACTIONr_mcangle_it0.972.3831983
X-RAY DIFFRACTIONr_mcangle_other0.9692.3851984
X-RAY DIFFRACTIONr_scbond_it0.861.6831763
X-RAY DIFFRACTIONr_scbond_other0.861.6841764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3732.4832576
X-RAY DIFFRACTIONr_long_range_B_refined4.09619.1894002
X-RAY DIFFRACTIONr_long_range_B_other3.80918.673928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 169 -
Rwork0.332 3057 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2182-0.2534-0.11631.6816-0.45811.21760.01240.02630.0448-0.0117-0.0583-0.1813-0.00580.18360.04590.0187-0.0108-0.00610.03520.01050.02286.64094.229517.4288
21.5673-0.04060.17111.8371-1.09221.70910.09680.0133-0.177-0.23850.02650.20320.2366-0.1826-0.12330.058-0.0132-0.04320.0283-0.00260.0459-20.1118-9.553815.8994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 199
2X-RAY DIFFRACTION2B2 - 199

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